I know that you can press CTRL + F a bunch of times to get to PAL60, but is there a bit of code that you can put in a game that would tell Stella to use PAL60 so players wouldn't have to play around with the settings?

When you finalize the PAL60 version you'll need to send stephena the final ROM and proper settings to use. He'll add the settings to Stella so that its next release will use the ROM's MD5 value to automatically use PAL60.

In the mean time, if the users do this then their copy of Stella will remember the custom setting:

hit TAB to bring up the in-game menu

Select Game Properties (you can see the ROM's MD5 value on the Cartridge Tab)

Select the Display Tab

Change Format from Auto-detect to PAL60

From then on, any time that ROM (as identified by the MD5 value) is loaded it will use PAL60.